The concept of this boss encounter is different compared to other bosses in both games. The player does not need to hit eight times traditionally, but the encounter is more about surviving. The main goal of the boss is for the player to keep chasing the doctor in his Egg Mobile across the very rugged and dangerous route, that has numerous obstacles from the zone which are able to damage the player. At the same time, the water also keeps raising below, as the player can have even more difficulties to avoid obstacles and most of all, the player is able to drown.

This Robotnik encounter is perhaps the most unique, but also the hardest boss encounter in the 16-bit version of Sonic the Hedgehog. After the player has climb on the long upper tunnel in Labyrinth Zone Act 3, he/she will suddenly come across to Dr. Robotnik on the right of cave, who after second starts flying with his mobile to the another upper tunnel. This one, however, is much more booby-trapped with annoying obstacles from the zone, such as moving spears and fire statues. The tunnel also is narrower and steeper as well.

Unlike the other bosses in the game, this mobile is unmodified and possesses no weaponry. Dr. Robotnik merely uses it to escape the flooding tunnels of the Labyrinth Zone. Sonic does not actually need to hit the mobile in order to complete the zone; he merely follows Dr. Robotnik through an ascending passage with fire statues and spear traps, while at the same time attempting to stay ahead of the rising water. There are no air bubbles in this tunnel section of the zone, and if the player becomes submerged, it can be difficult to recover ground. While Dr. Robotnik does not need to be attacked, a skillful player can make the mobile explode as usual after hitting eight times to it. In the Sonic Mega Collection Plus port of the game, the player needs to hit the mobile three times for it to explode.[citation needed]

Once the player reaches the top of the passage, Dr. Robotnik will fly away regardless. After opening the capsule, the player heads to the next zone.

The encounter of the Egg Mobile is later seen again as a boss in Sonic the Hedgehog 4: Episode I at the end of Lost Labyrinth Zone. At the start of the boss act, the player has to pick up some rings and head to the Dr. Eggman who, after laughing, flies away stage right. The route is more wheeling and smoother than before. Like its previous appearance, there are also numerous booby-trapped obstacles like spears, but there are also Badniks as well on the way. Despite the smoother platforming sections, the water once again rises below, while like in original Sonic the Hedgehog, there are no air bubbles on the route, as the player has to pass quickly as possible without drowning. The player is also able to attack the Egg Mobile by doing Homing Attack into it.

After being bounced to the air via spring, the player chases Eggman on the linear arena until the second phase of the boss battle starts and where the things start getting different. Eggman summons two pillars to rise from the ground, enclosing him and the player. Eggman then summons numerous different looking pillars slowly as attempting to crush the player, while the doctor himself flees to the safer place. The player has to head to the same place as well to survive and manage to hit Eggman at the same time. Eggman repeats doing this with different patterns until the player has defeated him, while the player should also memorize patterns and the doctor's moving directions.

After doing four hits into the Egg Mobile, all pillars disappear around the arena, while Eggman flees away with his damaged Egg Mobile. The player is then allowed to to open the capsule and complete the zone. This battle later reappears at E.G.G. Station Zone as a part of the boss rush before the final boss. While the chase section is not included, it moves to the newer part of the battle, where all pillar patterns are similar but replaced with high-tech ones to fit the space-themed zone. After another four hits, all pillars disappear and the player can move to the next boss.

Trivia

Before the player faces Robotnik in the original Sonic the Hedgehog, the Shieldmonitor is seen on left side of the cave, which can be helpful during the chase.

Strangely, in the iPod (click wheel) port of the original Sonic the Hedgehog, a glitch causes the water to stop rising at a certain point, making the chase significantly easier.

The boss encounter is more of a psychological boss than a physical one. It is not too easy to drown in, even if the player takes their time.

During the second phase in Sonic the Hedgehog 4: Episode I, the way the block pillars rise from the ground and the way Sonic has to stand on something to reach Dr. Robotnik is similar to the Hammer Eggman boss of Aquatic Ruin Zone in Sonic the Hedgehog 2.

In Sonic the Hedgehog 4, it is possible to hit Eggman before the battle really starts, standing on one of the walls that rise at the beginning of the battle and quickly doing a Homing Attack into him.